From dceac420dffa3aa74ef49a50d9be01e450e9d339 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Tue, 21 Jul 2020 11:05:00 +0100 Subject: Add sequencer JSON/XML output --- test/rest-api.org | 14 +++++++++++--- 1 file changed, 11 insertions(+), 3 deletions(-) (limited to 'test') diff --git a/test/rest-api.org b/test/rest-api.org index 1930d8b..6dd6616 100644 --- a/test/rest-api.org +++ b/test/rest-api.org @@ -53,12 +53,11 @@ When you use the search box on PubSeq it queries the REST end point for information on the search items. For example #+begin_src python :session :exports both -requests.get(baseURL+"/api/search?s=MT326090.1").json() +requests.get(baseURL+"/api/search?s=MT533203.1").json() #+end_src #+RESULTS: -| collection | : | http://collections.lugli.arvadosapi.com/c=10eaef75e0b875f81aa1f411c75370cf+126 | fasta | : | http://collections.lugli.arvadosapi.com/c=10eaef75e0b875f81aa1f411c75370cf+126/sequence.fasta | id | : | MT326090.1 | info | : | http://identifiers.org/insdc/MT326090.1#sequence | -| collection | : | http://collections.lugli.arvadosapi.com/c=5a4c815f3e076ad7760a91864c39dd07+126 | fasta | : | http://collections.lugli.arvadosapi.com/c=5a4c815f3e076ad7760a91864c39dd07+126/sequence.fasta | id | : | MT326090.1 | info | : | http://identifiers.org/insdc/MT326090.1#sequence | +| collection | : | http://collections.lugli.arvadosapi.com/c=0015b0d65dfd2e82bb3cee4436bf2893+126 | fasta | : | http://collections.lugli.arvadosapi.com/c=0015b0d65dfd2e82bb3cee4436bf2893+126/sequence.fasta | id | : | MT533203.1 | info | : | http://identifiers.org/insdc/MT533203.1#sequence | where collection is the raw uploaded data. The hash value in ~c=~ is computed on the contents of the Arvados keep [[https://doc.arvados.org/v2.0/user/tutorials/tutorial-keep-mount-gnu-linux.html][collection]] and effectively @@ -66,10 +65,19 @@ acts as a deduplication uuid. ** Fetch metadata +Using above collection link you can fetch the metadata in JSON as it +was uploaded originally from the SHeX expression, e.g. using +https://collections.lugli.arvadosapi.com/c=0015b0d65dfd2e82bb3cee4436bf2893+126/ + +But better to use the more advanced sample metadata fetcher +because is does a bit more in terms of expansion #+begin_src python :session :exports both +requests.get(baseURL+"/api/sample/MT533203.1.json").json() #+end_src +#+RESULTS: + ** Fetch EBI XML -- cgit v1.2.3